Genome-wide identification of MAPK, MAPKK, and MAPKKK gene families and transcriptional profiling analysis during development and stress response in cucumber.

Jie Wang,Lifei Chen,Yan Wang,Tao Zou,Gang Lu,Jian Wu,Lei Ye,Changtian Pan

doi:10.1186/s12864-015-1621-2

Abstract

BackgroundThe mitogen-activated protein kinase (MAPK) cascade consists of three types of reversibly phosphorylated kinases, namely, MAPK, MAPK kinase (MAPKK/MEK), and MAPK kinase kinase (MAPKKK/MEKK), playing important roles in plant growth, development, and defense response. The MAPK cascade genes have been investigated in detail in model plants, including Arabidopsis, rice, and tomato, but poorly characterized in cucumber (Cucumis sativus L.), a major popular vegetable in Cucurbitaceae crops, which is highly susceptible to environmental stress and pathogen attack.ResultsA genome-wide analysis revealed the presence of at least 14 MAPKs, 6 MAPKKs, and 59 MAPKKKs in the cucumber genome. Phylogenetic analyses classified all the CsMAPK and CsMAPKK genes into four groups, whereas the CsMAPKKK genes were grouped into the MEKK, RAF, and ZIK subfamilies. The expansion of these three gene families was mainly contributed by segmental duplication events. Furthermore, the ratios of non-synonymous substitution rates (Ka) and synonymous substitution rates (Ks) implied that the duplicated gene pairs had experienced strong purifying selection. Real-time PCR analysis demonstrated that some MAPK, MAPKK and MAPKKK genes are preferentially expressed in specific organs or tissues. Moreover, the expression levels of most of these genes significantly changed under heat, cold, drought, and Pseudoperonospora cubensis treatments. Exposure to abscisic acid and jasmonic acid markedly affected the expression levels of these genes, thereby implying that they may play important roles in the plant hormone network.ConclusionA comprehensive genome-wide analysis of gene structure, chromosomal distribution, and evolutionary relationship of MAPK cascade genes in cucumber are present here. Further expression analysis revealed that these genes were involved in important signaling pathways for biotic and abiotic stress responses in cucumber, as well as the response to plant hormones. Our first systematic description of the MAPK, MAPKK, and MAPKKK families in cucumber will help to elucidate their biological roles in plant.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1621-2) contains supplementary material, which is available to authorized users.

Highlights

The mitogen-activated protein kinase (MAPK) cascade consists of three types of reversibly phosphorylated kinases, namely, MAPK, MAPK kinase (MAPKK/MEK), and MAPK kinase kinase (MAPKKK/MEKK), playing important roles in plant growth, development, and defense response
Identification of the MAPK, MAPKK, and MAPKK kinase (MAPKKK) families in cucumber To identify MAPK, MAPKK and MAPKKK family genes, we conducted respective BLASTP searches against the cucumber protein database using query protein sequences including 143 MAPKs, 67 MAPKKs, and 534 MAPKKKs from seven plant species, which resulted in 602 hits
After multiple steps of screening and validation of the conserved domains, we identified 14 CsMAPK, 6 CsMAPKK, and 59 CsMAPKKK genes, respectively

Summary

Introduction

The mitogen-activated protein kinase (MAPK) cascade consists of three types of reversibly phosphorylated kinases, namely, MAPK, MAPK kinase (MAPKK/MEK), and MAPK kinase kinase (MAPKKK/MEKK), playing important roles in plant growth, development, and defense response. The mitogen-activated protein kinase (MAPK) signaling cascade has emerged as a universal signal transduction module that connects diverse receptors/sensors to cellular and nuclear responses in eukaryotes [12]. The classical MAPK signaling cascade is minimally composed of three kinases, namely, MAPK, MAPK kinase (MAPKK), and MAPKK kinase (MAPKKK) [13] These kinases operate as sequential signal transducers that channel, integrate, and amplify information from the cellular environment to transcriptional and metabolic response centers via phosphorylation. MAPKKs, in turn, are activated by MAPKKKs when the serine and serine/threonine residues in the S/TXXXXXS/T motif are phosphorylated [12]

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